Comparison of three different RNA extraction kits for transcriptome analysis of Indonesian rice (Oryza sativa L) explant for anther culture

Abstract

Recalcitrancy is the main problem in rice anther culture, especially in an Indica subspecies. It is well known that recalcitrancy is genotype dependent, and the effort to tackle this problem is mostly in the manipulations of media. Uncovering the genes responsible for recalcitrancy will benefit to enhance the success of this technique to accelerate the breeding process of Indonesian rice varieties which mostly belong to the indica subspecies. RNA-Seq is considered one of the best approaches to finding candidate genes responsible for specific traits including recalcitrant in anther culture. The aim of this study was to obtain the high concentration and good quality of RNA extracted methods using various extraction kits. The RNA extraction was carried out using Tripure, Promega, and RibospinTM Plant (Geneall) kit methods. Quality of RNA provided by the Promega kit showed good quality of RNA in all three genotypes tested ranging from 2.06±0.01-2.11±0.00 for A260/280 and 1.86±0.14-1.95±0.10 for A260/230.